Peutz-Jeghers syndrome (PJS) is characterized by gastrointestinal polyposis, mucocutaneous pigmentation and cancer predisposition. Patients with PJS can develop large calcifying Sertoli cell tumors (LCSTs). A patient presented at 3 years of age with delayed development, hypermobility and later also with tall stature and advanced bone age. Extensive endocrine evaluation, mutation analysis of genes associated with connective tissue disorders and a single nucleotide polymorphism (SNP) array showed no abnormalities. At 8 years of age, gynecomastia developed as well as pigmentations on the lips, both of which are associated with PJS. Mutation analysis showed a heterozygous deletion of the whole STK11 gene confirming PJS. Testicular ultrasound confirmed the presence of LCSTs. Interestingly, the previously performed SNP array did not report deletion of the STK11 gene. We advise excluding LCSTs in children with tall stature and advanced bone age where more common causes have been eliminated. Although STK11 deletions are documented in control databases, reporting the deletion of this gene even in the absence of a phenotype is advised for patient management.